Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1798
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 290850
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 2
Found at i:5705 original size:19 final size:19
Alignment explanation
Indices: 5681--5720 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5671 AGCTCCCATG
5681 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
5700 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
5719 TA
1 TA
5721 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:6178 original size:20 final size:20
Alignment explanation
Indices: 6132--6178 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
6122 AGCTCGTTTC
*
6132 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
6152 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
6172 CAGCTCA
1 CAGCTCA
6179 ATCTAACCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:7719 original size:23 final size:23
Alignment explanation
Indices: 7693--7757 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
7683 ATTGAAATTC
* *
7693 AAAAA-AAAAAAGAAGTGAGCAA
1 AAAAAGAAAAAAAAAGTGAACAA
7715 AAAAAGAAAAAAAAA--GAACAA
1 AAAAAGAAAAAAAAAGTGAACAA
7736 AAAAAGAACAAAAAAAAGTGAA
1 AAAAAG-A-AAAAAAAAGTGAA
7758 AAGTCTTGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
21 11 0.31
22 6 0.17
23 16 0.44
25 3 0.08
ACGTcount: A:0.78, C:0.05, G:0.14, T:0.03
Consensus pattern (23 bp):
AAAAAGAAAAAAAAAGTGAACAA
Found at i:7728 original size:10 final size:11
Alignment explanation
Indices: 7712--7751 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
7702 AAGAAGTGAG
7712 CAAAAAAAGAA
1 CAAAAAAAGAA
7723 -AAAAAAAGAA
1 CAAAAAAAGAA
7733 CAAAAAAAGAA
1 CAAAAAAAGAA
7744 CAAAAAAA
1 CAAAAAAA
7752 AGTGAAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.85, C:0.07, G:0.07, T:0.00
Consensus pattern (11 bp):
CAAAAAAAGAA
Found at i:10591 original size:20 final size:20
Alignment explanation
Indices: 10545--10591 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
10535 TAGCTGTTTC
*
10545 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
10565 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
10585 CAGCTCA
1 CAGCTCA
10592 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:15015 original size:22 final size:22
Alignment explanation
Indices: 14964--15029 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
14954 GGTATTTGGG
* *
14964 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
14985 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
15007 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
15030 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:19719 original size:22 final size:22
Alignment explanation
Indices: 19668--19733 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
19658 GGTATTTGGG
* * *
19668 AATTGGTTCGAACTAGTATGG-
1 AATTGGTACGAAATGGTATGGT
19689 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
19711 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
19734 TCAAAGAGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
21 18 0.47
22 15 0.39
23 5 0.13
ACGTcount: A:0.29, C:0.06, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:21631 original size:30 final size:30
Alignment explanation
Indices: 21597--21693 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
21587 TAAACTAAAA
21597 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
21627 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
*
21657 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGGTTTAGCTCGTGAGCT-AAAGT
21687 TGAGCTA
1 TGAGCTA
21694 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
30 48 0.94
31 3 0.06
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:23807 original size:15 final size:14
Alignment explanation
Indices: 23789--23851 Score: 55
Period size: 12 Copynumber: 4.6 Consensus size: 14
23779 GAATCACTCG
23789 TTTCTTTTATTTCAA
1 TTTCTTTT-TTTCAA
23804 TTTCTTTCTCTTT-AA
1 TTTCTTT-T-TTTCAA
23819 TTTC--TTTTTCAA
1 TTTCTTTTTTTCAA
23831 TTTC--TTTTTCAA
1 TTTCTTTTTTTCAA
*
23843 CTTCTTTTT
1 TTTCTTTTT
23852 CTCTCTCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
11 3 0.07
12 18 0.43
13 1 0.02
14 3 0.07
15 13 0.31
16 4 0.10
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTCTTTTTTTCAA
Found at i:23834 original size:12 final size:12
Alignment explanation
Indices: 23798--23852 Score: 65
Period size: 12 Copynumber: 4.3 Consensus size: 12
23788 GTTTCTTTTA
23798 TTTCAATTTCTTT
1 TTTCAATTTC-TT
*
23811 CTCTTTAATTTCTT
1 -T-TTCAATTTCTT
23825 TTTCAATTTCTT
1 TTTCAATTTCTT
*
23837 TTTCAACTTCTT
1 TTTCAATTTCTT
23849 TTTC
1 TTTC
23853 TCTCTCAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
12 25 0.68
13 1 0.03
14 3 0.08
15 8 0.22
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTCAATTTCTT
Found at i:23929 original size:12 final size:12
Alignment explanation
Indices: 23914--23944 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
23904 TTATTTTTGC
23914 TTTTCAAAGGCT
1 TTTTCAAAGGCT
*
23926 TTTTTAAAGGCT
1 TTTTCAAAGGCT
23938 TTTTCAA
1 TTTTCAA
23945 GTTCTCTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:24018 original size:5 final size:5
Alignment explanation
Indices: 23994--24048 Score: 51
Period size: 5 Copynumber: 10.6 Consensus size: 5
23984 CTTGCCTCTA
*
23994 TTTTC TTTT- TATTTC ATTTTC TTTT- TCTTC TTTTGC TTTTTC TTTTC
1 TTTTC TTTTC T-TTTC -TTTTC TTTTC TTTTC TTTT-C -TTTTC TTTTC
24041 TTTTC TTT
1 TTTTC TTT
24049 GTTTTCTCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
4 4 0.10
5 27 0.64
6 6 0.14
7 5 0.12
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:24032 original size:15 final size:14
Alignment explanation
Indices: 23994--24048 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 14
23984 CTTGCCTCTA
*
23994 TTTTCTTTTTATTTC
1 TTTTCTTTTT-CTTC
24009 ATTTTCTTTTTCTTC
1 -TTTTCTTTTTCTTC
24024 TTTTGCTTTTTCTTTTC
1 TTTT-CTTTTTC--TTC
24041 TTTTCTTT
1 TTTTCTTT
24049 GTTTTCTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
14 4 0.11
15 10 0.29
16 14 0.40
17 7 0.20
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (14 bp):
TTTTCTTTTTCTTC
Found at i:24049 original size:21 final size:20
Alignment explanation
Indices: 24010--24059 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 20
24000 TTTTATTTCA
24010 TTTTCTTTTTCTTCTTTTGCT
1 TTTTCTTTTTCTTCTTTTG-T
*
24031 TTTTC-TTTTCTTTTCTTTGT
1 TTTTCTTTTTCTTCT-TTTGT
24051 TTTCTCTTT
1 TTT-TCTTT
24060 ACAAGAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 12 0.48
21 11 0.44
22 2 0.08
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (20 bp):
TTTTCTTTTTCTTCTTTTGT
Found at i:26640 original size:30 final size:30
Alignment explanation
Indices: 26606--26702 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
26596 TAAACTAAAA
26606 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * *
26636 TGAGCTGAGGCTAAACTCCTAAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
*
26666 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGGTTTAGCTCGTGAGCT-AAAGT
26696 TGAGCTA
1 TGAGCTA
26703 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
30 49 0.92
31 4 0.08
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:27166 original size:20 final size:20
Alignment explanation
Indices: 27120--27166 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
27110 AGCTCGTTTC
*
27120 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
27140 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
27160 CAGCTCA
1 CAGCTCA
27167 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:30015 original size:22 final size:22
Alignment explanation
Indices: 29985--30028 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
29975 TTTGGTATTT
29985 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
30007 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
30029 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:33697 original size:18 final size:20
Alignment explanation
Indices: 33653--33713 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
33643 TTTCAATCTC
* *
33653 ATCACTCATTTTTTTTCTTTT
1 ATCACTCA-TCTTTTTGTTTT
33674 GAATCACTC-TCTTTTT-TTTT
1 --ATCACTCATCTTTTTGTTTT
33694 ATCACTCATCTTTTTGTTTT
1 ATCACTCATCTTTTTGTTTT
33714 TCTTCTTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
18 7 0.20
19 7 0.20
20 8 0.23
21 6 0.17
23 7 0.20
ACGTcount: A:0.15, C:0.20, G:0.03, T:0.62
Consensus pattern (20 bp):
ATCACTCATCTTTTTGTTTT
Found at i:38071 original size:29 final size:29
Alignment explanation
Indices: 38038--38094 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
38028 ATAACCAAAC
* *
38038 CTACAAAAACTTTATATCCATAAACCCAA
1 CTACAAAAACTTCATATACATAAACCCAA
*
38067 CTACATAAACTTCATATACATAAACCCA
1 CTACAAAAACTTCATATACATAAACCCA
38095 TCTTTGAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (29 bp):
CTACAAAAACTTCATATACATAAACCCAA
Found at i:39398 original size:21 final size:21
Alignment explanation
Indices: 39372--39434 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
39362 TTGGTATTTG
39372 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
39393 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
39414 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
39435 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:43016 original size:29 final size:29
Alignment explanation
Indices: 42983--43042 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
42973 ATAACCAAAC
* *
42983 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCACAAACCCAT
*
43012 CTACATAAACTTCATATCCACAAACCCAT
1 CTACAAAAACTTCATATCCACAAACCCAT
43041 CT
1 CT
43043 TTAAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.27
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCACAAACCCAT
Found at i:47941 original size:14 final size:14
Alignment explanation
Indices: 47899--47943 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
47889 TTAAAGAGGC
47899 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
47913 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
47926 AACTCATTTAATTA
1 AACTCATTAAATTA
47940 AACT
1 AACT
47944 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:50454 original size:12 final size:11
Alignment explanation
Indices: 50421--50450 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
50411 TTGTAGATTC
50421 AAAAAAAATTG
1 AAAAAAAATTG
50432 AAAAAAAATTG
1 AAAAAAAATTG
50443 AAAAAAAA
1 AAAAAAAA
50451 ATTGCATACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:57516 original size:30 final size:30
Alignment explanation
Indices: 57430--57527 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
57420 TTAAACTAAA
* *
57430 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * *
57460 TTGAGCTGAGATTAAACTCTTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
57490 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
57520 ATGAGCTA
1 ATGAGCTA
57528 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:57867 original size:21 final size:21
Alignment explanation
Indices: 57843--57891 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
57833 TATACAAGTT
*
57843 AAAAAAATTTGAAAAAAATTC
1 AAAAAAATTTGAAAAAAACTC
*
57864 AAAAAAATTTGAAAAAAACTG
1 AAAAAAATTTGAAAAAAACTC
57885 AAAAAAA
1 AAAAAAA
57892 GGTGTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.18
Consensus pattern (21 bp):
AAAAAAATTTGAAAAAAACTC
Found at i:57891 original size:10 final size:10
Alignment explanation
Indices: 57843--57891 Score: 62
Period size: 10 Copynumber: 4.7 Consensus size: 10
57833 TATACAAGTT
57843 AAAAAAATTTG
1 AAAAAAA-TTG
*
57854 AAAAAAATTC
1 AAAAAAATTG
57864 AAAAAAATTTG
1 AAAAAAA-TTG
*
57875 AAAAAAACTG
1 AAAAAAATTG
57885 AAAAAAA
1 AAAAAAA
57892 GGTGTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
10 18 0.53
11 16 0.47
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.18
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:58813 original size:5 final size:5
Alignment explanation
Indices: 58797--58858 Score: 60
Period size: 5 Copynumber: 12.6 Consensus size: 5
58787 TCTTGTAAAT
*
58797 AGAAA A-AAA AGAAA AGAAA AGAAA A-AGA A-AAA AGAAAA AGAAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AG-AAA AG-AAA AGAAA
58846 TA-AAA AGAAA AGA
1 -AGAAA AGAAA AGA
58859 GAGGCAAGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
4 11 0.22
5 27 0.54
6 12 0.24
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (5 bp):
AGAAA
Found at i:58856 original size:6 final size:6
Alignment explanation
Indices: 58802--58845 Score: 65
Period size: 6 Copynumber: 7.5 Consensus size: 6
58792 TAAATAGAAA
58802 AAAAAG -AAAAG -AAAAG AAAAAG AAAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAAG AAAAAG AAAAAG AAA
58846 TAAAAAGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 10 0.28
6 20 0.56
7 6 0.17
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:58927 original size:12 final size:12
Alignment explanation
Indices: 58906--58936 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
58896 TTGAGAGAAC
*
58906 TTGAAGAAGCCT
1 TTGAAAAAGCCT
58918 TTGAAAAAGCCT
1 TTGAAAAAGCCT
58930 TTGAAAA
1 TTGAAAA
58937 GCAAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:58949 original size:7 final size:6
Alignment explanation
Indices: 58933--58988 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
58923 AAAGCCTTTG
* * ** *
58933 AAAAGCA AAAAGA AAAAGA AAAAGA AAATGA GATTGA AAAAGA GAAAG-
1 AAAAG-A AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
58981 AAAAGA AA
1 AAAAGA AA
58989 TTTGAGAGTG
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
5 4 0.10
6 31 0.77
7 5 0.12
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.05
Consensus pattern (6 bp):
AAAAGA
Found at i:58973 original size:30 final size:30
Alignment explanation
Indices: 58939--59006 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
58929 TTTGAAAAGC
*
58939 AAAAAGAAAAAGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAAAG-AAAAGAAATATGAGAGTG
* *
58969 AAAAAGAGAAAGAAAAGAAATTTGAGAGTG
1 AAAAAGAAAAAGAAAAGAAATATGAGAGTG
58999 AAAAAGAA
1 AAAAAGAA
59007 GTTGAAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 8 0.24
30 25 0.76
ACGTcount: A:0.68, C:0.00, G:0.22, T:0.10
Consensus pattern (30 bp):
AAAAAGAAAAAGAAAAGAAATATGAGAGTG
Found at i:58993 original size:24 final size:24
Alignment explanation
Indices: 58944--58990 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
58934 AAAGCAAAAA
*
58944 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAATGAAATT
*
58968 GAAAAAGAGAAAGAAAA-GAAATT
1 GAAAAAGAAAAAGAAAATGAAATT
58991 TGAGAGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.11
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAATGAAATT
Found at i:59014 original size:12 final size:12
Alignment explanation
Indices: 58997--59042 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
58987 AATTTGAGAG
*
58997 TGAAAAAGAAGT
1 TGAAAAAGAAAT
59009 TGAAAAAGAAAT
1 TGAAAAAGAAAT
*
59021 TGAAAAAGAGAT
1 TGAAAAAGAAAT
*
59033 T-AAAGAGAAA
1 TGAAAAAGAAA
59043 GAAATTGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
11 7 0.23
12 23 0.77
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (12 bp):
TGAAAAAGAAAT
Found at i:61290 original size:10 final size:10
Alignment explanation
Indices: 61277--61323 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
61267 AAGCTCTGTC
*
61277 CAGCTCAATT
1 CAGCTCATTT
61287 CAGCTCATTT
1 CAGCTCATTT
* *
61297 GAGTTCATTT
1 CAGCTCATTT
61307 CAGCTCATTT
1 CAGCTCATTT
*
61317 GAGCTCA
1 CAGCTCA
61324 ACTATGCTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (10 bp):
CAGCTCATTT
Found at i:67796 original size:20 final size:20
Alignment explanation
Indices: 67750--67796 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
67740 AGCTCGTTTC
*
67750 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
67770 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
67790 CAGCTCA
1 CAGCTCA
67797 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:74441 original size:6 final size:6
Alignment explanation
Indices: 74430--74465 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
74420 TTCAATTTTT
* *
74430 TCTCAA TATCAA TATCAA TCTCAA TCTCAA TCTCAA
1 TCTCAA TCTCAA TCTCAA TCTCAA TCTCAA TCTCAA
74466 ATTCTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.39, C:0.28, G:0.00, T:0.33
Consensus pattern (6 bp):
TCTCAA
Found at i:74517 original size:21 final size:20
Alignment explanation
Indices: 74473--74517 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
74463 CAAATTCTTT
*
74473 TTTCTTTTTCTCACTCTCAT
1 TTTCTTTTTCTCACTCTCAA
* *
74493 TTTCTTTTTTTCTTCTCTCAA
1 TTTCTTTTTCTC-ACTCTCAA
74514 TTTC
1 TTTC
74518 ATTCAAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCTTTTTCTCACTCTCAA
Found at i:75359 original size:31 final size:30
Alignment explanation
Indices: 75321--75391 Score: 106
Period size: 30 Copynumber: 2.3 Consensus size: 30
75311 ATTTCAATCA
** *
75321 CTTTTTTTTTTCAATTTTGATTTTTTTTCTT
1 CTTTTTTTTTT-AATTTCAATTTTTTTTATT
75352 CTTTTTTTTTTAATTTCAATTTTTTTTATT
1 CTTTTTTTTTTAATTTCAATTTTTTTTATT
75382 CTTTTTTTTT
1 CTTTTTTTTT
75392 CTTCAATACT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 26 0.70
31 11 0.30
ACGTcount: A:0.11, C:0.08, G:0.01, T:0.79
Consensus pattern (30 bp):
CTTTTTTTTTTAATTTCAATTTTTTTTATT
Found at i:75453 original size:14 final size:14
Alignment explanation
Indices: 75431--75470 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
75421 AAATTGAATA
*
75431 CAAACTTTTTTTTT
1 CAAAATTTTTTTTT
75445 CAAAATTTTTTTTT
1 CAAAATTTTTTTTT
*
75459 C-GAATTTTTTTT
1 CAAAATTTTTTTT
75471 ATATTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.65
Consensus pattern (14 bp):
CAAAATTTTTTTTT
Found at i:79623 original size:10 final size:10
Alignment explanation
Indices: 79607--79664 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
79597 AAACTCCGAC
79607 CAGCTCAATT
1 CAGCTCAATT
* *
79617 GAGCTCATTT
1 CAGCTCAATT
79627 CAGCTCAA-T
1 CAGCTCAATT
79636 CGAGCTCAATT
1 C-AGCTCAATT
*
79647 TAGCTACAATT
1 CAGCT-CAATT
79658 CAGCTCA
1 CAGCTCA
79665 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:79630 original size:20 final size:20
Alignment explanation
Indices: 79607--79667 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
79597 AAACTCCGAC
79607 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
79627 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
79648 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
79668 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:89829 original size:10 final size:10
Alignment explanation
Indices: 89816--89855 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
89806 AGCTCACTTG
89816 AGCTCGTTTT
1 AGCTCGTTTT
*
89826 AGCTCGTTTC
1 AGCTCGTTTT
*
89836 AGCTCGAATTT
1 AGCTCG-TTTT
89847 AGCTCGTTT
1 AGCTCGTTT
89856 CAGTTCATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:90104 original size:13 final size:13
Alignment explanation
Indices: 90086--90114 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
90076 AATAGTTGTG
90086 TGTTATTTAATTA
1 TGTTATTTAATTA
90099 TGTTATTTAATTA
1 TGTTATTTAATTA
90112 TGT
1 TGT
90115 AGGTTAACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:107822 original size:30 final size:30
Alignment explanation
Indices: 107786--107882 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
107776 TGCTCACTCC
107786 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
107816 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
107846 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
107876 TAGCTCA
1 TAGCTCA
107883 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:109623 original size:42 final size:42
Alignment explanation
Indices: 109562--109657 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 42
109552 GATTATGAGG
* * * *
109562 GAAAATGAGAGGATTTTGAATGAAATCGAGAGAAGAAACAAA
1 GAAAATGAGAGAATCTTGAATGAAATCAAGAAAAGAAACAAA
109604 GAAAATGAGAGAATCTTGAATGAAATCAAGAAAAGAAACAAA
1 GAAAATGAGAGAATCTTGAATGAAATCAAGAAAAGAAACAAA
*
109646 G-AAATGAAAGAA
1 GAAAATGAGAGAA
109658 AAAGAAAATG
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 10 0.20
42 39 0.80
ACGTcount: A:0.57, C:0.05, G:0.23, T:0.15
Consensus pattern (42 bp):
GAAAATGAGAGAATCTTGAATGAAATCAAGAAAAGAAACAAA
Found at i:109687 original size:24 final size:24
Alignment explanation
Indices: 109655--109735 Score: 99
Period size: 24 Copynumber: 3.4 Consensus size: 24
109645 AGAAATGAAA
109655 GAAAAAGAAAATGAGATTGAGAGT
1 GAAAAAGAAAATGAGATTGAGAGT
* *
109679 GAAAAAGAAAATGAGATTGAAAAT
1 GAAAAAGAAAATGAGATTGAGAGT
* * * * *
109703 GAGAATGAAAAAGAGTTTGAGAGA
1 GAAAAAGAAAATGAGATTGAGAGT
109727 GAAAAAGAA
1 GAAAAAGAA
109736 TGTGAACAAG
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (24 bp):
GAAAAAGAAAATGAGATTGAGAGT
Found at i:109688 original size:30 final size:30
Alignment explanation
Indices: 109652--109716 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
109642 CAAAGAAATG
* * *
109652 AAAGAAAAAGAAAATGAGATTGAGAGTGAA
1 AAAGAAAAAGAAAATGAAAATGAGAATGAA
* * *
109682 AAAGAAAATGAGATTGAAAATGAGAATGAA
1 AAAGAAAAAGAAAATGAAAATGAGAATGAA
109712 AAAGA
1 AAAGA
109717 GTTTGAGAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.25, T:0.14
Consensus pattern (30 bp):
AAAGAAAAAGAAAATGAAAATGAGAATGAA
Found at i:109702 original size:12 final size:12
Alignment explanation
Indices: 109661--109713 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
109651 GAAAGAAAAA
*
109661 GAAAATGAGATT
1 GAAAATGAGAAT
* * * *
109673 GAGAGTGAAAAA
1 GAAAATGAGAAT
*
109685 GAAAATGAGATT
1 GAAAATGAGAAT
109697 GAAAATGAGAAT
1 GAAAATGAGAAT
109709 GAAAA
1 GAAAA
109714 AGAGTTTGAG
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.57, C:0.00, G:0.26, T:0.17
Consensus pattern (12 bp):
GAAAATGAGAAT
Found at i:109709 original size:18 final size:18
Alignment explanation
Indices: 109661--109710 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
109651 GAAAGAAAAA
*
109661 GAAAATGAGATTGAGAGT
1 GAAAATGAGAATGAGAGT
* * *
109679 GAAAAAGAAAATGAGATT
1 GAAAATGAGAATGAGAGT
109697 GAAAATGAGAATGA
1 GAAAATGAGAATGA
109711 AAAAGAGTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.54, C:0.00, G:0.28, T:0.18
Consensus pattern (18 bp):
GAAAATGAGAATGAGAGT
Found at i:109764 original size:18 final size:19
Alignment explanation
Indices: 109728--109766 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
109718 TTTGAGAGAG
*
109728 AAAAAGAATGTGAACAAGA
1 AAAAAGAATGTGAAAAAGA
*
109747 AAAAAGAGTG-GAAAAAGA
1 AAAAAGAATGTGAAAAAGA
109765 AA
1 AA
109767 TTGAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.08
Consensus pattern (19 bp):
AAAAAGAATGTGAAAAAGA
Found at i:117333 original size:4 final size:4
Alignment explanation
Indices: 117324--117351 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
117314 AAGTTTTATT
117324 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
117352 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:120743 original size:22 final size:22
Alignment explanation
Indices: 120713--120756 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
120703 TTTGGTATTT
120713 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
120735 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
120757 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:121385 original size:30 final size:30
Alignment explanation
Indices: 121351--121447 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
121341 AGCTCACTCC
121351 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
121381 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
121411 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
121441 TAGCTCA
1 TAGCTCA
121448 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:125306 original size:14 final size:14
Alignment explanation
Indices: 125259--125306 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
125249 GTACGAATGG
*
125259 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
125273 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
125287 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
125301 ATTGGT
1 AATGGT
125307 CGGTTTAGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:129839 original size:14 final size:14
Alignment explanation
Indices: 129817--129864 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
129807 ACCTAAACCG
* *
129817 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
129831 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
129845 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
129859 ACCATT
1 ACCATT
129865 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:130230 original size:9 final size:9
Alignment explanation
Indices: 130218--130259 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
130208 TATACAAGTT
130218 AAAAAAATA
1 AAAAAAATA
*
130227 AAAAAAATC
1 AAAAAAATA
*
130236 GAAAAAAT-
1 AAAAAAATA
130244 AAAAAAATA
1 AAAAAAATA
130253 AAAAAAA
1 AAAAAAA
130260 AGTGATTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 7 0.24
9 22 0.76
ACGTcount: A:0.86, C:0.02, G:0.02, T:0.10
Consensus pattern (9 bp):
AAAAAAATA
Found at i:130247 original size:7 final size:8
Alignment explanation
Indices: 130217--130258 Score: 57
Period size: 8 Copynumber: 5.0 Consensus size: 8
130207 TTATACAAGT
130217 TAAAAAAA
1 TAAAAAAA
130225 TAAAAAAAA
1 T-AAAAAAA
*
130234 TCGAAAAAA
1 T-AAAAAAA
130243 TAAAAAAA
1 TAAAAAAA
130251 TAAAAAAA
1 TAAAAAAA
130259 AAGTGATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
8 15 0.50
9 15 0.50
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.12
Consensus pattern (8 bp):
TAAAAAAA
Found at i:132946 original size:19 final size:19
Alignment explanation
Indices: 132922--132961 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
132912 AGCTCCCATG
132922 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
132941 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
132960 TA
1 TA
132962 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:134224 original size:14 final size:14
Alignment explanation
Indices: 134202--134249 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
134192 AACTAAACCG
* *
134202 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
134216 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
134230 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
134244 ACCATT
1 ACCATT
134250 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:145824 original size:100 final size:99
Alignment explanation
Indices: 145699--145881 Score: 323
Period size: 100 Copynumber: 1.8 Consensus size: 99
145689 GAAGCTATCT
*
145699 GGTACGCAAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCT-GTTACATGTAGTAGCC
1 GGTACGCAAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTAG-TACACGTAGTAGCC
*
145763 TGCACTTAGTACTACACACGTGATCACAGTTTTTG
65 TGCACTTAATACTACACACGTGATCACAGTTTTTG
145798 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTAGTACACGTAGTAGCC
1 GGTACGCA-AGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTAGTACACGTAGTAGCC
145863 TGCACTTAATACTACACAC
65 TGCACTTAATACTACACAC
145882 ATGACCTCAC
Statistics
Matches: 80, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
99 8 0.10
100 71 0.89
101 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (99 bp):
GGTACGCAAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTAGTACACGTAGTAGCCT
GCACTTAATACTACACACGTGATCACAGTTTTTG
Found at i:145829 original size:51 final size:48
Alignment explanation
Indices: 145696--145981 Score: 243
Period size: 51 Copynumber: 5.8 Consensus size: 48
145686 GCCGAAGCTA
* * *
145696 TCTGGTACGCA-AGTAGCCTGCACTTAGTACTACACATGCGACCAACAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC-ACAG
* ** *
145744 TCTGTTACATGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCACAG
* * * *
145792 TTTTTGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG
1 --TCT-GGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC-ACAG
* * * *
145844 TCTAGTACACGTAGTAGCCTGCACTTAATACTACACACATGACCTCACCA-
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA-C-CA-CAG
** * * * *
145894 TCTAATACACGTAGTAGCCTACAATTAGTACTACACACGTGATCACAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCACAG
* * *
145942 TTTTCGGGTACGCATAGTAGCTTGCACTTAGTACTACACA
1 ---TCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
145982 TGCGACCTCA
Statistics
Matches: 189, Mismatches: 37, Indels: 21
0.77 0.15 0.09
Matches are distributed among these distances:
47 2 0.01
48 13 0.07
49 61 0.32
50 43 0.23
51 66 0.35
52 4 0.02
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (48 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCACAG
Found at i:145906 original size:50 final size:49
Alignment explanation
Indices: 145707--145931 Score: 202
Period size: 49 Copynumber: 4.5 Consensus size: 49
145697 CTGGTACGCA
** ** *
145707 AGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGTTACATGT
1 AGTAGCCTGCACTTAGTACTACACACACGACCAACAGTCTAATACACGT
** * * ** * *
145756 AGTAGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTTGGGTACGCAT
1 AGTAGCCTGCACTTAGTACTACACACACGACCAACAG--TCT-AATACACGT
** *
145807 AGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTAGTACACGT
1 AGTAGCCTGCACTTAGTACTACACACACGACCAACAGTCTAATACACGT
* * *
145856 AGTAGCCTGCACTTAATACTACACACATGACCTCACCA-TCTAATACACGT
1 AGTAGCCTGCACTTAGTACTACACACACGA-C-CAACAGTCTAATACACGT
* *
145906 AGTAGCCTACAATTAGTACTACACAC
1 AGTAGCCTGCACTTAGTACTACACAC
145932 GTGATCACAG
Statistics
Matches: 146, Mismatches: 24, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
48 4 0.03
49 61 0.42
50 39 0.27
51 38 0.26
52 4 0.03
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (49 bp):
AGTAGCCTGCACTTAGTACTACACACACGACCAACAGTCTAATACACGT
Found at i:149280 original size:20 final size:20
Alignment explanation
Indices: 149243--149292 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
149233 AAGAAGCGAG
*
149243 AAAAAGAAATTGAGAGAAGAA
1 AAAAAGAAATGGAGAGAA-AA
*
149264 AAAAAGACATGGA-AGAAAA
1 AAAAAGAAATGGAGAGAAAA
149283 AGAAAAGAAA
1 A-AAAAGAAA
149293 ATAAAAAGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 3 0.12
20 11 0.44
21 11 0.44
ACGTcount: A:0.70, C:0.02, G:0.22, T:0.06
Consensus pattern (20 bp):
AAAAAGAAATGGAGAGAAAA
Found at i:151103 original size:42 final size:42
Alignment explanation
Indices: 151053--151228 Score: 169
Period size: 42 Copynumber: 4.0 Consensus size: 42
151043 CTTCATTTTC
** * *
151053 TCGATGCCATAGTTCAACTATGGTCTTAGACATCTTCACATAA
1 TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACAT-A
* *
151096 T-GATGCCATAGCCCAGCTATGATCTTACACATATTCACATA
1 TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACATA
*
151137 TCGATGCCATGGCCCAACTATGGTCTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAACTATGGTCTTACAC---AT---AT-TCACATA
* *
151186 TCGATGCCATAGCCCAGCTATGGCCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAACTATGGTCTTACAC-ATATTCACATA
151227 TC
1 TC
151229 TCACTGATGT
Statistics
Matches: 112, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
41 11 0.10
42 59 0.53
43 2 0.02
45 2 0.02
47 1 0.01
48 2 0.02
49 35 0.31
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (42 bp):
TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACATA
Found at i:151201 original size:49 final size:49
Alignment explanation
Indices: 151123--151380 Score: 224
Period size: 47 Copynumber: 5.2 Consensus size: 49
151113 TATGATCTTA
* *
151123 CACATATTCACATATCGATGCCATGGCCCAACTATGGTCTTACACGTAAT
1 CACATA-TCACATATCGATGCCATAGCCCAACTATGGTCTTATACGTAAT
* * *
151173 CACATATCACATATCGATGCCATAGCCCAGCTATGGCCTTACACG-AAT
1 CACATATCACATATCGATGCCATAGCCCAACTATGGTCTTATACGTAAT
* * * * *
151221 CACATATCTCA-CT-GATGTCATATCCCAGA-TATGGTCTTATACAGT-AG
1 CACATATCACATATCGATGCCATAGCCCA-ACTATGGTCTTATAC-GTAAT
* * * * * * *
151268 CATATATCAC--ACCGATGCCATATCACAAATATGGTCTTATACGGAAG
1 CACATATCACATATCGATGCCATAGCCCAACTATGGTCTTATACGTAAT
* *
151315 CACATAATCACATCTGTCCGATGCCATAGCCCAACTATGGTCTTATACGGAAAT
1 CACAT-ATCACA--TAT-CGATGCCATAGCCCAACTATGGTCTTATAC-GTAAT
151369 CACATATCACAT
1 CACATATCACAT
151381 GTTGCCATGG
Statistics
Matches: 169, Mismatches: 26, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
46 25 0.15
47 42 0.25
48 18 0.11
49 36 0.21
50 6 0.04
51 1 0.01
53 33 0.20
54 8 0.05
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (49 bp):
CACATATCACATATCGATGCCATAGCCCAACTATGGTCTTATACGTAAT
Found at i:151354 original size:53 final size:53
Alignment explanation
Indices: 151279--151380 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
151269 ATATATCACA
*
151279 CCGATGCCATATCACAAATATGGTCTTATACGG-AAGCACATAATCACATCTGT
1 CCGATGCCATAGCACAAATATGGTCTTATACGGAAAGCACAT-ATCACATCTGT
* * *
151332 CCGATGCCATAGCCCAACTATGGTCTTATACGGAAATCACATATCACAT
1 CCGATGCCATAGCACAAATATGGTCTTATACGGAAAGCACATATCACAT
151381 GTTGCCATGG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 37 0.84
54 7 0.16
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.25
Consensus pattern (53 bp):
CCGATGCCATAGCACAAATATGGTCTTATACGGAAAGCACATATCACATCTGT
Found at i:156666 original size:23 final size:22
Alignment explanation
Indices: 156614--156666 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
156604 TCCACGTCTT
*
156614 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
156636 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
156659 TTTCTTTT
1 TTTCTTTT
156667 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:161007 original size:42 final size:42
Alignment explanation
Indices: 160944--161107 Score: 195
Period size: 42 Copynumber: 3.7 Consensus size: 42
160934 CTTTGTTTTC
** *
160944 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACAT-A
* *
160987 T-GATGCCATAGCCCAGCTATGATCTTACACATATTCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATA
*
161028 TCGATGCCATGGCCCAGCTATGGTCTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC---AT--C-T-TCACATA
161077 TCGATGCCATAGCCCAGCTATGGTCTTACAC
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC
161108 GAATCACGTA
Statistics
Matches: 104, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
41 2 0.02
42 61 0.59
43 1 0.01
45 2 0.02
48 1 0.01
49 37 0.36
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.29
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATA
Found at i:161239 original size:53 final size:47
Alignment explanation
Indices: 161014--161270 Score: 194
Period size: 47 Copynumber: 5.3 Consensus size: 47
161004 TATGATCTTA
* ** * * * *
161014 CACATATTCACATATCGATGCCATGGCCCAGCTATGGTCTTACACGTAAT
1 CACATA-TCACATCT-GATGCCATATCCCAGATATGGTCTTATA-GGAAG
* * * * * *
161064 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGAAT
1 CACATATCACATCT-GATGCCATATCCCAGATATGGTCTTATAGGAAG
* * * * *
161112 CACGTATCTCA-CTAATGCCATATCCCAGATATGGTCTTATATAGTAG
1 CACATATCACATCTGATGCCATATCCCAGATATGGTCTTATA-GGAAG
*
161159 CATATATCACA-CTGATGCCATATCCCAGATATGGTCTTATACGGAAG
1 CACATATCACATCTGATGCCATATCCCAGATATGGTCTTATA-GGAAG
* * *
161206 CACATAATCACATCTCTCCGATGCCATAGCCCAGCTATGGTCTTATAGGAAAT
1 CACAT-ATCACA--TCT--GATGCCATATCCCAGATATGGTCTTATAGG-AAG
161259 CACATATCACAT
1 CACATATCACAT
161271 GTTGCCATGG
Statistics
Matches: 175, Mismatches: 24, Indels: 16
0.81 0.11 0.07
Matches are distributed among these distances:
46 24 0.14
47 47 0.27
48 18 0.10
49 36 0.21
50 7 0.04
51 2 0.01
52 8 0.05
53 33 0.19
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.28
Consensus pattern (47 bp):
CACATATCACATCTGATGCCATATCCCAGATATGGTCTTATAGGAAG
Found at i:168946 original size:20 final size:20
Alignment explanation
Indices: 168900--168946 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
168890 AGCTCGTTTC
*
168900 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
168920 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
168940 CAGCTCA
1 CAGCTCA
168947 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:173852 original size:13 final size:12
Alignment explanation
Indices: 173811--173855 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
173801 ATTGAGAGTG
173811 AAAAGAA-TGTGA
1 AAAAGAAGT-TGA
*
173823 AAAAGAAATTGA
1 AAAAGAAGTTGA
173835 AAAAGAAGTTGA
1 AAAAGAAGTTGA
173847 AGAAAGAAG
1 A-AAAGAAG
173856 AGAAAATGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 22 0.73
13 8 0.27
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.13
Consensus pattern (12 bp):
AAAAGAAGTTGA
Found at i:175256 original size:12 final size:13
Alignment explanation
Indices: 175229--175261 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
175219 GTTGTAAAGT
*
175229 TTTATTTTTATTA
1 TTTATTTATATTA
175242 TTTATTTAT-TTA
1 TTTATTTATATTA
175254 TTTATTTA
1 TTTATTTA
175262 CTTAGTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTATATTA
Found at i:179159 original size:30 final size:30
Alignment explanation
Indices: 179125--179222 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 30
179115 AGCTCACTCC
179125 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
179155 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * * *
179185 CATCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
179215 TAGCTCAT
1 TAGCTCAT
179223 TTTAGTTTAA
Statistics
Matches: 48, Mismatches: 18, Indels: 3
0.70 0.26 0.04
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:180763 original size:14 final size:14
Alignment explanation
Indices: 180716--180763 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
180706 GTACGAATGG
*
180716 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
180730 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
180744 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
180758 ATTGGT
1 AATGGT
180764 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:187271 original size:10 final size:10
Alignment explanation
Indices: 187256--187310 Score: 62
Period size: 10 Copynumber: 5.7 Consensus size: 10
187246 ATAAATCACT
187256 TTTTTTTCGA
1 TTTTTTTCGA
187266 -TTTTTT--A
1 TTTTTTTCGA
187273 TTTTTTTTCGA
1 -TTTTTTTCGA
*
187284 TTTTTTTTGA
1 TTTTTTTCGA
*
187294 TTTTTTTTGA
1 TTTTTTTCGA
187304 TTTTTTT
1 TTTTTTT
187311 TAACTTGTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
7 1 0.03
9 12 0.30
10 26 0.65
11 1 0.03
ACGTcount: A:0.09, C:0.04, G:0.07, T:0.80
Consensus pattern (10 bp):
TTTTTTTCGA
Found at i:187278 original size:18 final size:19
Alignment explanation
Indices: 187255--187309 Score: 78
Period size: 18 Copynumber: 2.9 Consensus size: 19
187245 CATAAATCAC
187255 TTTTTTTTCGATTTTTT-A
1 TTTTTTTTCGATTTTTTGA
187273 TTTTTTTTCGATTTTTTTTGA
1 TTTTTTTTCGA--TTTTTTGA
187294 TTTTTTTT-GATTTTTT
1 TTTTTTTTCGATTTTTT
187310 TTAACTTGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 17 0.50
20 8 0.24
21 9 0.26
ACGTcount: A:0.09, C:0.04, G:0.07, T:0.80
Consensus pattern (19 bp):
TTTTTTTTCGATTTTTTGA
Found at i:187310 original size:20 final size:20
Alignment explanation
Indices: 187255--187312 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
187245 CATAAATCAC
187255 TTTTTTTTCGA--TTTTTTA
1 TTTTTTTTCGATTTTTTTTA
187273 TTTTTTTTCGATTTTTTTTGA
1 TTTTTTTTCGATTTTTTTT-A
187294 TTTTTTTT-GATTTTTTTTA
1 TTTTTTTTCGATTTTTTTTA
187313 ACTTGTATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 11 0.30
19 1 0.03
20 16 0.43
21 9 0.24
ACGTcount: A:0.10, C:0.03, G:0.07, T:0.79
Consensus pattern (20 bp):
TTTTTTTTCGATTTTTTTTA
Found at i:187311 original size:10 final size:10
Alignment explanation
Indices: 187266--187311 Score: 76
Period size: 10 Copynumber: 4.6 Consensus size: 10
187256 TTTTTTTCGA
187266 TTTTTT-ATT
1 TTTTTTGATT
187275 TTTTTTCGATT
1 TTTTTT-GATT
187286 TTTTTTGATT
1 TTTTTTGATT
187296 TTTTTTGATT
1 TTTTTTGATT
187306 TTTTTT
1 TTTTTT
187312 AACTTGTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
9 6 0.17
10 20 0.57
11 9 0.26
ACGTcount: A:0.09, C:0.02, G:0.07, T:0.83
Consensus pattern (10 bp):
TTTTTTGATT
Found at i:187694 original size:14 final size:14
Alignment explanation
Indices: 187660--187707 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
187650 GTACAAATGG
**
187660 AATGGTAGGAATGA
1 AATGGTAGGAACAA
*
187674 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
187688 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
187702 ATTGGT
1 AATGGT
187708 CGGTTTAGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.31, T:0.21
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:189664 original size:17 final size:18
Alignment explanation
Indices: 189642--189684 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
189632 ACATATTAAT
189642 AACAAATATTAAT-ATAA
1 AACAAATATTAATGATAA
*
189659 AACAAAT-TTAATGATTA
1 AACAAATATTAATGATAA
*
189676 AATAAATAT
1 AACAAATAT
189685 ATTCGAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 5 0.23
17 16 0.73
18 1 0.05
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (18 bp):
AACAAATATTAATGATAA
Found at i:194063 original size:21 final size:21
Alignment explanation
Indices: 194019--194079 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
194009 CTCACAAGAC
*
194019 TTTTTCACTTTTTTTTGTTCT
1 TTTTTCACTTTTTTTTCTTCT
*
194040 TTTTTTACTTTTTTTTACTT-T
1 TTTTTCACTTTTTTTT-CTTCT
194061 TTTTGCTCACTTCTTTTTT
1 TTTT--TCACTT-TTTTTT
194080 TTTTTGAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 20 0.61
22 2 0.06
23 5 0.15
24 6 0.18
ACGTcount: A:0.07, C:0.15, G:0.03, T:0.75
Consensus pattern (21 bp):
TTTTTCACTTTTTTTTCTTCT
Found at i:195635 original size:20 final size:20
Alignment explanation
Indices: 195612--195658 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
195602 GGGTTCAGAT
*
195612 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
195632 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
195652 TGAGCTG
1 TGAGCTG
195659 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:199822 original size:17 final size:17
Alignment explanation
Indices: 199802--199896 Score: 52
Period size: 17 Copynumber: 5.4 Consensus size: 17
199792 TTTTTCAATT
199802 TTCTTTTCTTTCTCACA
1 TTCTTTTCTTTCTCACA
199819 TTCTTTT-TTGCTCTCA-A
1 TTCTTTTCTT--TCTCACA
**
199836 TCTCTTTTTACTTTCTTTCA
1 T-TC-TTTT-CTTTCTCACA
* *
199856 TTCTTTT-TTTTTCAATA
1 TTCTTTTCTTTCTC-ACA
* *
199873 TTTTTTTCTTTTTCACA
1 TTCTTTTCTTTCTCACA
*
199890 TGCTTTT
1 TTCTTTT
199897 TTATTTCATT
Statistics
Matches: 59, Mismatches: 10, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
16 6 0.10
17 23 0.39
18 17 0.29
19 9 0.15
20 2 0.03
21 2 0.03
ACGTcount: A:0.12, C:0.21, G:0.02, T:0.65
Consensus pattern (17 bp):
TTCTTTTCTTTCTCACA
Found at i:199826 original size:18 final size:18
Alignment explanation
Indices: 199805--199897 Score: 61
Period size: 18 Copynumber: 5.2 Consensus size: 18
199795 TTCAATTTTC
199805 TTTTCTTTCTCACATTCT
1 TTTTCTTTCTCACATTCT
*
199823 TTTT-TGCTCTCA-ATCTCT
1 TTTTCT-TTCTCACAT-TCT
**
199841 TTTTACTTTCTTTCATTCT
1 TTTT-CTTTCTCACATTCT
*
199860 TTTT-TTT-TCA-ATATTT
1 TTTTCTTTCTCACAT-TCT
* *
199876 TTTTCTTTTTCACATGCT
1 TTTTCTTTCTCACATTCT
199894 TTTT
1 TTTT
199898 TATTTCATTA
Statistics
Matches: 57, Mismatches: 9, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
15 2 0.04
16 7 0.12
17 9 0.16
18 24 0.42
19 12 0.21
20 3 0.05
ACGTcount: A:0.12, C:0.20, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTTCTTTCTCACATTCT
Found at i:199850 original size:37 final size:33
Alignment explanation
Indices: 199787--199898 Score: 91
Period size: 34 Copynumber: 3.2 Consensus size: 33
199777 TCCAAACTCA
*
199787 CTTTCTTTT-TCAATTTTCTTTTCTTTCTCACATT
1 CTTT-TTTTCTCAATATT-TTTTCTTTCTCACATT
* **
199821 CTTTTTTGCTCTCAATCTCTTTTTACTTTCTTTCATT
1 CTTTTTT--TCTCAATAT-TTTTT-CTTTCTCACATT
* * *
199858 CTTTTTTTTTCAATATTTTTTTCTTTTTCACATG
1 CTTTTTTTCTCAATA-TTTTTTCTTTCTCACATT
199892 CTTTTTT
1 CTTTTTT
199899 ATTTCATTAC
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
33 3 0.05
34 19 0.30
35 12 0.19
36 11 0.17
37 18 0.29
ACGTcount: A:0.12, C:0.21, G:0.02, T:0.66
Consensus pattern (33 bp):
CTTTTTTTCTCAATATTTTTTCTTTCTCACATT
Found at i:200182 original size:28 final size:28
Alignment explanation
Indices: 200150--200203 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
200140 GAGTAGAAAG
**
200150 AAGGGTACGAATGAAATGGTAGGAACGA
1 AAGGGTACGAACAAAATGGTAGGAACGA
* *
200178 AAGGGTAGGAACAAAATGGTATGAAC
1 AAGGGTACGAACAAAATGGTAGGAAC
200204 AAATTGGTCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.44, C:0.07, G:0.33, T:0.15
Consensus pattern (28 bp):
AAGGGTACGAACAAAATGGTAGGAACGA
Found at i:200211 original size:14 final size:14
Alignment explanation
Indices: 200163--200211 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
200153 GGTACGAATG
*
200163 AAATGGTAGGAACG
1 AAATGGTAGGAACA
*
200177 AAAGGGTAGGAACA
1 AAATGGTAGGAACA
*
200191 AAATGGTATGAACA
1 AAATGGTAGGAACA
*
200205 AATTGGT
1 AAATGGT
200212 CGGTTTAGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.45, C:0.06, G:0.31, T:0.18
Consensus pattern (14 bp):
AAATGGTAGGAACA
Found at i:202133 original size:30 final size:31
Alignment explanation
Indices: 202099--202195 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
202089 AGCTCACTCC
*
202099 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
202129 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
202159 CAGCTCAACTTT-AGCTCACGAGCTAAAACT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
202189 TAGCTCA
1 TAGCTCA
202196 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:204766 original size:15 final size:14
Alignment explanation
Indices: 204735--204773 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
204725 AAGAGAAAAT
204735 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
204751 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
204766 AAAGAAAA
1 AAAGAAAA
204774 CGAAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 9 0.41
16 4 0.18
17 5 0.23
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:204853 original size:11 final size:12
Alignment explanation
Indices: 204839--204868 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
204829 TTGAGAGAAC
204839 TTGAAAAA-CCT
1 TTGAAAAAGCCT
204850 TTGAAAAAGCCT
1 TTGAAAAAGCCT
204862 TTGAAAA
1 TTGAAAA
204869 GCAAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:204903 original size:29 final size:31
Alignment explanation
Indices: 204871--204950 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 31
204861 TTTGAAAAGC
* *
204871 AAAAGAAAATGAAAAAGAAA-ATGAGATTG-
1 AAAAGAAAACGAAAAAGAAATATGAGAGTGA
* *
204900 AAAAGAGAACG-AAAAGAAATTTGAGAGTGA
1 AAAAGAAAACGAAAAAGAAATATGAGAGTGA
* *
204930 AAAAGAAGAGGAAAAAGAAAT
1 AAAAGAAAACGAAAAAGAAAT
204951 TGAAACAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
28 8 0.20
29 16 0.39
30 8 0.20
31 9 0.22
ACGTcount: A:0.64, C:0.01, G:0.24, T:0.11
Consensus pattern (31 bp):
AAAAGAAAACGAAAAAGAAATATGAGAGTGA
Found at i:204936 original size:28 final size:28
Alignment explanation
Indices: 204883--204936 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
204873 AAGAAAATGA
*
204883 AAAAGAAAATGAGATTGAAAAGAGAACG
1 AAAAGAAAATGAGAGTGAAAAGAGAACG
*
204911 AAAAGAAATTTGAGAGTGAAAA-AGAA
1 AAAAGAAA-ATGAGAGTGAAAAGAGAA
204937 GAGGAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.61, C:0.02, G:0.24, T:0.13
Consensus pattern (28 bp):
AAAAGAAAATGAGAGTGAAAAGAGAACG
Found at i:206562 original size:28 final size:29
Alignment explanation
Indices: 206497--206552 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
206487 GATTCAAAGA
*
206497 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
206526 TGGGTTTATGGATATAAAGTTT-TGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
206553 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:211164 original size:15 final size:15
Alignment explanation
Indices: 211144--211190 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
211134 TCAAAGATGG
211144 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* *
211159 GTTTATGTAGATG--
1 GTTTATGGATATGAA
*
211172 GTTTATGGATATAAA
1 GTTTATGGATATGAA
211187 GTTT
1 GTTT
211191 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
13 10 0.40
15 15 0.60
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.45
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:211179 original size:28 final size:29
Alignment explanation
Indices: 211138--211196 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
211128 AAGGATTCAA
*
211138 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
211167 AGAT-GGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
211195 AG
1 AG
211197 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:213318 original size:30 final size:31
Alignment explanation
Indices: 213284--213380 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
213274 AGCTCACTCC
*
213284 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
213314 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
213344 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
213374 TAGCTCA
1 TAGCTCA
213381 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:215910 original size:16 final size:16
Alignment explanation
Indices: 215891--215929 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
215881 AAGAGAAAAT
215891 AAAGAAAA-GAAAAGAA
1 AAAGAAAATG-AAAGAA
*
215907 AAAGAAAATGAAATAA
1 AAAGAAAATGAAAGAA
215923 AAAGAAA
1 AAAGAAA
215930 GAGAGGCAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.95
17 1 0.05
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (16 bp):
AAAGAAAATGAAAGAA
Found at i:216008 original size:11 final size:11
Alignment explanation
Indices: 215979--216009 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
215969 TTGAGAGAAC
*
215979 TTGAAAAACCT
1 TTGAAAAGCCT
215990 TTGAAAAGCCT
1 TTGAAAAGCCT
216001 TTGAAAAGC
1 TTGAAAAGC
216010 AAAAAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (11 bp):
TTGAAAAGCCT
Found at i:216025 original size:12 final size:12
Alignment explanation
Indices: 216010--216034 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
216000 TTTGAAAAGC
216010 AAAAAGAAAATG
1 AAAAAGAAAATG
216022 AAAAAGAAAATG
1 AAAAAGAAAATG
216034 A
1 A
216035 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:216031 original size:18 final size:18
Alignment explanation
Indices: 216004--216046 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
215994 AAAGCCTTTG
216004 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
216023 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
216041 AAAAGA
1 AAAAGA
216047 GAACAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:216044 original size:30 final size:31
Alignment explanation
Indices: 216010--216091 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
216000 TTTGAAAAGC
*
216010 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * * *
216040 AAAAAGAGAA-CAAAAATAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
216070 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
216092 TGAAACAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 8 0.20
30 24 0.59
31 9 0.22
ACGTcount: A:0.66, C:0.01, G:0.20, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:222300 original size:29 final size:29
Alignment explanation
Indices: 222234--222290 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
222224 GATTCAAAGA
*
222234 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
222263 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
222291 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:224432 original size:30 final size:31
Alignment explanation
Indices: 224398--224494 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
224388 AGCTCACTCC
*
224398 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
224428 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
224458 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
224488 TAGCTCA
1 TAGCTCA
224495 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:229114 original size:30 final size:30
Alignment explanation
Indices: 229029--229125 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
229019 TAAACTAAAA
* *
229029 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
229059 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
229089 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
229118 ATGAGCTA
1 -TGAGCTA
229126 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:235212 original size:20 final size:20
Alignment explanation
Indices: 235189--235235 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
235179 GGGTTAAGAT
*
235189 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
235209 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
235229 TGAGCTG
1 TGAGCTG
235236 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:236958 original size:48 final size:48
Alignment explanation
Indices: 236903--237008 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
236893 TTGTCTTTTC
*
236903 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
236951 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
236999 TTTCTTTTTC
1 TTTCTTTTTC
237009 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:240695 original size:20 final size:20
Alignment explanation
Indices: 240672--240718 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
240662 GGGTTAAGAT
*
240672 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
240692 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
240712 TGAGCTG
1 TGAGCTG
240719 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:240942 original size:14 final size:14
Alignment explanation
Indices: 240895--240942 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
240885 GTACGAATGG
*
240895 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
240909 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
240923 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
240937 ATTGGT
1 AATGGT
240943 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:250341 original size:13 final size:13
Alignment explanation
Indices: 250323--250347 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
250313 TGGTCATCAT
250323 GGTGTGAACACAA
1 GGTGTGAACACAA
250336 GGTGTGAACACA
1 GGTGTGAACACA
250348 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:251144 original size:30 final size:29
Alignment explanation
Indices: 251049--251145 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 29
251039 AGCTCACTCC
*
251049 TAGCTCATA-TTCAGCTCACAAGCTAAACTT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAAC-T
* * * *
251079 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAG-CTAAACT
* *
251109 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAA-CT
251139 TAGCTCA
1 TAGCTCA
251146 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 4 0.08
30 44 0.85
31 4 0.08
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (29 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACT
Found at i:254468 original size:18 final size:18
Alignment explanation
Indices: 254447--254504 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
254437 CCTCACTCTT
254447 TTTTTTGATTTCTTTTTC
1 TTTTTTGATTTCTTTTTC
** *
254465 TTTTTCAATCTCTTTTTC
1 TTTTTTGATTTCTTTTTC
254483 TTTTCTTTTGATTTCTTTTTC
1 --TT-TTTTGATTTCTTTTTC
254504 T
1 T
254505 CGCACGCACT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
18 15 0.48
19 1 0.03
20 2 0.06
21 13 0.42
ACGTcount: A:0.07, C:0.16, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTTTGATTTCTTTTTC
Found at i:255402 original size:11 final size:12
Alignment explanation
Indices: 255383--255416 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
255373 TTATACTTCA
255383 AATTTTTTTTTG
1 AATTTTTTTTTG
255395 AATTTTTTTTTG
1 AATTTTTTTTTG
255407 AATTTTTTTT
1 AATTTTTTTT
255417 CAAATTTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:255422 original size:12 final size:12
Alignment explanation
Indices: 255379--255423 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
255369 TTTTTTATAC
255379 TTCAAATTTTTT
1 TTCAAATTTTTT
**
255391 TTTGAATTTTTT
1 TTCAAATTTTTT
**
255403 TTTGAATTTTTT
1 TTCAAATTTTTT
255415 TTCAAATTT
1 TTCAAATTT
255424 CCTCTTCTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (12 bp):
TTCAAATTTTTT
Found at i:262481 original size:20 final size:20
Alignment explanation
Indices: 262456--262527 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
262446 TGTGGTTCAA
262456 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTTAG
* *
262476 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTTAG
* * *
262496 CTCATTCAAGCTCAATTTAA
1 CTCATTCGAGCTCAAGTTAG
262516 CTCATT-GAGCTC
1 CTCATTCGAGCTC
262528 GTTATTAGCT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 5 0.11
20 39 0.89
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTTAG
Found at i:262893 original size:45 final size:45
Alignment explanation
Indices: 262843--263036 Score: 289
Period size: 45 Copynumber: 4.3 Consensus size: 45
262833 GAACGGCATG
*
262843 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTTATGGAAC
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
* *
262888 AAATTAAGGAAGCACTTGACCAACATCATGCATAATTCATGGAAG
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
* * *
262933 AATTTGAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAG
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
* * * *
262978 AATTTAAGGAAGCATTTGGCCAACATCATGCATAATTTAAGGAAC
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
*
263023 AAATTGAGGAAGCA
1 AAATTAAGGAAGCA
263037 CCATGGCCGA
Statistics
Matches: 136, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 136 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (45 bp):
AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
Found at i:265924 original size:13 final size:13
Alignment explanation
Indices: 265906--265930 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
265896 TGGTCATCAT
265906 GGTGTGAACACAA
1 GGTGTGAACACAA
265919 GGTGTGAACACA
1 GGTGTGAACACA
265931 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:267887 original size:10 final size:10
Alignment explanation
Indices: 267872--267898 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
267862 TACTCCTTCA
267872 AGCTCAAATC
1 AGCTCAAATC
267882 AGCTCAAATC
1 AGCTCAAATC
267892 AGCTCAA
1 AGCTCAA
267899 CTTCAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:268575 original size:20 final size:20
Alignment explanation
Indices: 268529--268575 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
268519 AGCTCGTTTC
*
268529 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
268549 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
268569 CAGCTCA
1 CAGCTCA
268576 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:271272 original size:48 final size:47
Alignment explanation
Indices: 271193--271298 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
271183 GAGTGTCATG
*
271193 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
271241 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
271289 GAAAAAGAAA
1 GAAAAAGAAA
271299 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:273015 original size:20 final size:20
Alignment explanation
Indices: 272969--273015 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
272959 AGCTCGTTTC
*
272969 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
272989 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
273009 CAGCTCA
1 CAGCTCA
273016 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Done.